We've gone through a few design iterations for a solar power system in my group, but unfortunately we haven't gotten any concrete results. Solar power is viable on balloon flights because hopefully you'll be flying during the day and above the clouds, but it comes with some challenges:
1) Getting the electronics to work. We designed our solar payload from scratch, so a big part of it was avoid soldering errors and debugging everything properly. Especially with the multi power point tracking system, we ran into a lot of trouble.
2) Solar cell placement. Getting adequate sunlit area on your cells is hard because mounting area = weight. Basically, having a large enough exposure area to fully charge your batteries would mean that your payload box would be quite large. This is assuming you're using budget solar cells.
3) It's hard to maximize solar cell efficiency. As most payload boxes are box shaped, the overall efficiency of your array would be pretty bad if you mounted your cells on the outside surface of the box. You might be able to get away with mounting external panels and maybe even using sun tracking to actuate the array, but that comes with its own challenges...
That might not have been what you were looking for, I just decided to ramble a bit... I've been working a lot with solar power over the past year. I'll post some pictures of our actual solar payloads and write more about those later.